Starting phenix.real_space_refine (version: dev) on Mon Dec 12 22:38:55 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f2d_4173/12_2022/6f2d_4173.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f2d_4173/12_2022/6f2d_4173.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f2d_4173/12_2022/6f2d_4173.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f2d_4173/12_2022/6f2d_4173.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f2d_4173/12_2022/6f2d_4173.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f2d_4173/12_2022/6f2d_4173.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "E TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 12541 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1575 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 15, 'TRANS': 187} Chain: "B" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1575 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 15, 'TRANS': 187} Chain: "C" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1575 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 15, 'TRANS': 187} Chain: "D" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1575 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 15, 'TRANS': 187} Chain: "E" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1575 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 15, 'TRANS': 187} Chain: "F" Number of atoms: 1986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1986 Classifications: {'peptide': 258} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 240} Chain: "G" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 670 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "H" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 670 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "I" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 670 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "J" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 670 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Time building chain proxies: 7.39, per 1000 atoms: 0.59 Number of scatterers: 12541 At special positions: 0 Unit cell: (105.78, 107.5, 131.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 99 16.00 O 2118 8.00 N 1934 7.00 C 8390 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.90 Conformation dependent library (CDL) restraints added in 1.9 seconds 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3094 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 0 sheets defined 82.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 44 through 61 removed outlier: 4.414A pdb=" N THR A 52 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N PHE A 53 " --> pdb=" O THR A 49 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU A 54 " --> pdb=" O SER A 50 " (cutoff:3.500A) Proline residue: A 55 - end of helix Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.801A pdb=" N ILE A 68 " --> pdb=" O PHE A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 101 removed outlier: 4.043A pdb=" N THR A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 112 Processing helix chain 'A' and resid 112 through 117 Processing helix chain 'A' and resid 126 through 142 Proline residue: A 133 - end of helix removed outlier: 4.094A pdb=" N GLN A 141 " --> pdb=" O PHE A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 154 removed outlier: 3.571A pdb=" N LEU A 147 " --> pdb=" O ARG A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 207 removed outlier: 3.522A pdb=" N LEU A 170 " --> pdb=" O PRO A 166 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 171 " --> pdb=" O MET A 167 " (cutoff:3.500A) Proline residue: A 172 - end of helix removed outlier: 3.883A pdb=" N GLN A 184 " --> pdb=" O LYS A 180 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N THR A 188 " --> pdb=" O GLN A 184 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 190 " --> pdb=" O GLY A 186 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE A 191 " --> pdb=" O PHE A 187 " (cutoff:3.500A) Proline residue: A 192 - end of helix removed outlier: 3.706A pdb=" N LEU A 207 " --> pdb=" O VAL A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 228 Proline residue: A 220 - end of helix removed outlier: 3.675A pdb=" N PHE A 226 " --> pdb=" O LYS A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 245 removed outlier: 3.820A pdb=" N PHE A 243 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TYR A 244 " --> pdb=" O ALA A 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 62 removed outlier: 3.969A pdb=" N PHE B 53 " --> pdb=" O THR B 49 " (cutoff:3.500A) Proline residue: B 55 - end of helix removed outlier: 3.658A pdb=" N LEU B 59 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 77 removed outlier: 3.585A pdb=" N ILE B 69 " --> pdb=" O THR B 65 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN B 76 " --> pdb=" O GLY B 72 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 101 removed outlier: 3.536A pdb=" N THR B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 112 Processing helix chain 'B' and resid 112 through 119 removed outlier: 4.221A pdb=" N GLU B 118 " --> pdb=" O GLN B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 142 removed outlier: 3.744A pdb=" N ASP B 128 " --> pdb=" O GLN B 124 " (cutoff:3.500A) Proline residue: B 133 - end of helix removed outlier: 3.697A pdb=" N GLN B 141 " --> pdb=" O PHE B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 155 removed outlier: 4.101A pdb=" N LEU B 147 " --> pdb=" O ARG B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 207 Proline residue: B 172 - end of helix removed outlier: 3.936A pdb=" N PHE B 190 " --> pdb=" O GLY B 186 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE B 191 " --> pdb=" O PHE B 187 " (cutoff:3.500A) Proline residue: B 192 - end of helix removed outlier: 3.913A pdb=" N LEU B 207 " --> pdb=" O VAL B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 228 removed outlier: 4.141A pdb=" N ILE B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) Proline residue: B 220 - end of helix removed outlier: 3.815A pdb=" N PHE B 226 " --> pdb=" O LYS B 222 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 245 removed outlier: 4.065A pdb=" N VAL B 236 " --> pdb=" O TRP B 232 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TYR B 244 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER B 245 " --> pdb=" O GLN B 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 61 Proline residue: C 55 - end of helix Processing helix chain 'C' and resid 64 through 75 removed outlier: 3.877A pdb=" N VAL C 70 " --> pdb=" O ARG C 66 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE C 71 " --> pdb=" O ILE C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 101 removed outlier: 3.715A pdb=" N GLY C 91 " --> pdb=" O GLN C 87 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR C 97 " --> pdb=" O ALA C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 112 Processing helix chain 'C' and resid 112 through 117 Processing helix chain 'C' and resid 123 through 141 removed outlier: 4.120A pdb=" N LEU C 127 " --> pdb=" O MET C 123 " (cutoff:3.500A) Proline residue: C 133 - end of helix removed outlier: 4.118A pdb=" N GLN C 141 " --> pdb=" O PHE C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 155 removed outlier: 3.687A pdb=" N ALA C 148 " --> pdb=" O GLU C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 207 Proline residue: C 172 - end of helix removed outlier: 4.022A pdb=" N PHE C 190 " --> pdb=" O GLY C 186 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ILE C 191 " --> pdb=" O PHE C 187 " (cutoff:3.500A) Proline residue: C 192 - end of helix Processing helix chain 'C' and resid 214 through 228 removed outlier: 3.615A pdb=" N ALA C 218 " --> pdb=" O PRO C 214 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU C 219 " --> pdb=" O ALA C 215 " (cutoff:3.500A) Proline residue: C 220 - end of helix removed outlier: 3.597A pdb=" N PHE C 226 " --> pdb=" O LYS C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 244 removed outlier: 3.846A pdb=" N VAL C 236 " --> pdb=" O TRP C 232 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N TYR C 244 " --> pdb=" O ALA C 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 61 removed outlier: 4.025A pdb=" N PHE D 53 " --> pdb=" O THR D 49 " (cutoff:3.500A) Proline residue: D 55 - end of helix Processing helix chain 'D' and resid 64 through 75 removed outlier: 3.528A pdb=" N ARG D 75 " --> pdb=" O PHE D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 112 removed outlier: 3.591A pdb=" N THR D 97 " --> pdb=" O ALA D 93 " (cutoff:3.500A) Proline residue: D 103 - end of helix Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 124 through 142 removed outlier: 3.723A pdb=" N ASP D 128 " --> pdb=" O GLN D 124 " (cutoff:3.500A) Proline residue: D 133 - end of helix Processing helix chain 'D' and resid 143 through 154 removed outlier: 4.014A pdb=" N LEU D 147 " --> pdb=" O ARG D 143 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA D 148 " --> pdb=" O GLU D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 208 removed outlier: 3.921A pdb=" N LEU D 171 " --> pdb=" O MET D 167 " (cutoff:3.500A) Proline residue: D 172 - end of helix removed outlier: 3.864A pdb=" N PHE D 190 " --> pdb=" O GLY D 186 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE D 191 " --> pdb=" O PHE D 187 " (cutoff:3.500A) Proline residue: D 192 - end of helix Processing helix chain 'D' and resid 213 through 218 Processing helix chain 'D' and resid 218 through 228 Processing helix chain 'D' and resid 231 through 245 removed outlier: 3.783A pdb=" N VAL D 236 " --> pdb=" O TRP D 232 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA D 240 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE D 243 " --> pdb=" O LEU D 239 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR D 244 " --> pdb=" O ALA D 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 61 Proline residue: E 55 - end of helix removed outlier: 3.943A pdb=" N LEU E 59 " --> pdb=" O PRO E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 77 removed outlier: 4.310A pdb=" N ILE E 69 " --> pdb=" O THR E 65 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL E 70 " --> pdb=" O ARG E 66 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE E 71 " --> pdb=" O ILE E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 112 removed outlier: 3.931A pdb=" N ALA E 93 " --> pdb=" O LEU E 89 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR E 97 " --> pdb=" O ALA E 93 " (cutoff:3.500A) Proline residue: E 103 - end of helix Processing helix chain 'E' and resid 112 through 117 Processing helix chain 'E' and resid 124 through 142 Proline residue: E 133 - end of helix removed outlier: 3.884A pdb=" N GLN E 141 " --> pdb=" O PHE E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 154 removed outlier: 3.627A pdb=" N ALA E 148 " --> pdb=" O GLU E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 207 removed outlier: 4.081A pdb=" N LEU E 170 " --> pdb=" O PRO E 166 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU E 171 " --> pdb=" O MET E 167 " (cutoff:3.500A) Proline residue: E 172 - end of helix removed outlier: 3.726A pdb=" N ILE E 191 " --> pdb=" O PHE E 187 " (cutoff:3.500A) Proline residue: E 192 - end of helix removed outlier: 3.604A pdb=" N LEU E 207 " --> pdb=" O VAL E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 228 removed outlier: 4.305A pdb=" N PHE E 221 " --> pdb=" O ILE E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 242 Processing helix chain 'F' and resid 7 through 16 removed outlier: 3.900A pdb=" N TRP F 12 " --> pdb=" O GLN F 8 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N TYR F 16 " --> pdb=" O TRP F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 29 Processing helix chain 'F' and resid 39 through 44 Processing helix chain 'F' and resid 44 through 55 removed outlier: 4.366A pdb=" N ILE F 48 " --> pdb=" O LEU F 44 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU F 52 " --> pdb=" O ILE F 48 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL F 53 " --> pdb=" O MET F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 104 removed outlier: 3.840A pdb=" N GLN F 76 " --> pdb=" O TRP F 72 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN F 77 " --> pdb=" O LEU F 73 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE F 78 " --> pdb=" O ALA F 74 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU F 79 " --> pdb=" O MET F 75 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE F 80 " --> pdb=" O GLN F 76 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY F 85 " --> pdb=" O GLY F 81 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N PHE F 90 " --> pdb=" O PHE F 86 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ALA F 91 " --> pdb=" O THR F 87 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE F 92 " --> pdb=" O MET F 88 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE F 101 " --> pdb=" O THR F 97 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE F 102 " --> pdb=" O ALA F 98 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY F 103 " --> pdb=" O GLY F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 106 No H-bonds generated for 'chain 'F' and resid 105 through 106' Processing helix chain 'F' and resid 107 through 112 removed outlier: 4.071A pdb=" N PHE F 110 " --> pdb=" O GLY F 107 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA F 111 " --> pdb=" O LEU F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 137 removed outlier: 3.875A pdb=" N MET F 129 " --> pdb=" O LEU F 125 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET F 131 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA F 133 " --> pdb=" O MET F 129 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N MET F 134 " --> pdb=" O ASP F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 157 removed outlier: 3.564A pdb=" N HIS F 155 " --> pdb=" O VAL F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 175 removed outlier: 3.721A pdb=" N ALA F 171 " --> pdb=" O ASN F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 208 removed outlier: 3.923A pdb=" N LEU F 181 " --> pdb=" O GLY F 177 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU F 186 " --> pdb=" O ASN F 182 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA F 187 " --> pdb=" O GLY F 183 " (cutoff:3.500A) Proline residue: F 189 - end of helix removed outlier: 3.989A pdb=" N THR F 196 " --> pdb=" O THR F 192 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU F 197 " --> pdb=" O LEU F 193 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY F 202 " --> pdb=" O ASN F 198 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU F 204 " --> pdb=" O ALA F 200 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASN F 205 " --> pdb=" O LEU F 201 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ARG F 206 " --> pdb=" O GLY F 202 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N MET F 207 " --> pdb=" O LEU F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 215 Processing helix chain 'F' and resid 216 through 232 removed outlier: 3.635A pdb=" N LEU F 220 " --> pdb=" O ILE F 216 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N THR F 223 " --> pdb=" O PRO F 219 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL F 224 " --> pdb=" O LEU F 220 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET F 229 " --> pdb=" O GLY F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 261 removed outlier: 3.607A pdb=" N PHE F 239 " --> pdb=" O LEU F 235 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLU F 241 " --> pdb=" O ALA F 237 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N HIS F 242 " --> pdb=" O PRO F 238 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU F 243 " --> pdb=" O PHE F 239 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE F 247 " --> pdb=" O LEU F 243 " (cutoff:3.500A) Proline residue: F 259 - end of helix Processing helix chain 'G' and resid 2 through 39 removed outlier: 3.640A pdb=" N GLY G 10 " --> pdb=" O VAL G 6 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS G 15 " --> pdb=" O THR G 11 " (cutoff:3.500A) Proline residue: G 23 - end of helix Processing helix chain 'G' and resid 50 through 65 removed outlier: 3.526A pdb=" N VAL G 58 " --> pdb=" O LYS G 54 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE G 63 " --> pdb=" O PHE G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 88 removed outlier: 3.628A pdb=" N LEU G 70 " --> pdb=" O GLY G 66 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU G 73 " --> pdb=" O MET G 69 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG G 78 " --> pdb=" O LEU G 74 " (cutoff:3.500A) Proline residue: G 85 - end of helix removed outlier: 3.586A pdb=" N ILE G 88 " --> pdb=" O LEU G 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 39 removed outlier: 3.640A pdb=" N GLY H 10 " --> pdb=" O VAL H 6 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS H 15 " --> pdb=" O THR H 11 " (cutoff:3.500A) Proline residue: H 23 - end of helix Processing helix chain 'H' and resid 50 through 65 removed outlier: 3.525A pdb=" N VAL H 58 " --> pdb=" O LYS H 54 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE H 63 " --> pdb=" O PHE H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 88 removed outlier: 3.629A pdb=" N LEU H 70 " --> pdb=" O GLY H 66 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU H 73 " --> pdb=" O MET H 69 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG H 78 " --> pdb=" O LEU H 74 " (cutoff:3.500A) Proline residue: H 85 - end of helix removed outlier: 3.586A pdb=" N ILE H 88 " --> pdb=" O LEU H 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 39 removed outlier: 3.640A pdb=" N GLY I 10 " --> pdb=" O VAL I 6 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS I 15 " --> pdb=" O THR I 11 " (cutoff:3.500A) Proline residue: I 23 - end of helix Processing helix chain 'I' and resid 50 through 65 removed outlier: 3.526A pdb=" N VAL I 58 " --> pdb=" O LYS I 54 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE I 63 " --> pdb=" O PHE I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 88 removed outlier: 3.628A pdb=" N LEU I 70 " --> pdb=" O GLY I 66 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU I 73 " --> pdb=" O MET I 69 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG I 78 " --> pdb=" O LEU I 74 " (cutoff:3.500A) Proline residue: I 85 - end of helix removed outlier: 3.586A pdb=" N ILE I 88 " --> pdb=" O LEU I 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 39 removed outlier: 3.640A pdb=" N GLY J 10 " --> pdb=" O VAL J 6 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS J 15 " --> pdb=" O THR J 11 " (cutoff:3.500A) Proline residue: J 23 - end of helix Processing helix chain 'J' and resid 50 through 65 removed outlier: 3.526A pdb=" N VAL J 58 " --> pdb=" O LYS J 54 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE J 63 " --> pdb=" O PHE J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 88 removed outlier: 3.628A pdb=" N LEU J 70 " --> pdb=" O GLY J 66 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU J 73 " --> pdb=" O MET J 69 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG J 78 " --> pdb=" O LEU J 74 " (cutoff:3.500A) Proline residue: J 85 - end of helix removed outlier: 3.586A pdb=" N ILE J 88 " --> pdb=" O LEU J 84 " (cutoff:3.500A) 787 hydrogen bonds defined for protein. 2346 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.30 Time building geometry restraints manager: 6.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3742 1.34 - 1.46: 2363 1.46 - 1.58: 6518 1.58 - 1.70: 0 1.70 - 1.81: 197 Bond restraints: 12820 Sorted by residual: bond pdb=" C LEU F 58 " pdb=" N PRO F 59 " ideal model delta sigma weight residual 1.334 1.218 0.115 2.34e-02 1.83e+03 2.43e+01 bond pdb=" CG ARG B 75 " pdb=" CD ARG B 75 " ideal model delta sigma weight residual 1.520 1.439 0.081 3.00e-02 1.11e+03 7.28e+00 bond pdb=" C THR J 2 " pdb=" N PRO J 3 " ideal model delta sigma weight residual 1.335 1.304 0.030 1.19e-02 7.06e+03 6.53e+00 bond pdb=" C THR H 2 " pdb=" N PRO H 3 " ideal model delta sigma weight residual 1.335 1.304 0.030 1.19e-02 7.06e+03 6.42e+00 bond pdb=" C THR G 2 " pdb=" N PRO G 3 " ideal model delta sigma weight residual 1.335 1.305 0.030 1.19e-02 7.06e+03 6.30e+00 ... (remaining 12815 not shown) Histogram of bond angle deviations from ideal: 95.91 - 103.57: 336 103.57 - 111.23: 5811 111.23 - 118.89: 4760 118.89 - 126.55: 6417 126.55 - 134.21: 152 Bond angle restraints: 17476 Sorted by residual: angle pdb=" C ASN J 45 " pdb=" N GLU J 46 " pdb=" CA GLU J 46 " ideal model delta sigma weight residual 121.98 113.11 8.87 1.35e+00 5.49e-01 4.32e+01 angle pdb=" C ASN G 45 " pdb=" N GLU G 46 " pdb=" CA GLU G 46 " ideal model delta sigma weight residual 121.98 113.12 8.86 1.35e+00 5.49e-01 4.30e+01 angle pdb=" C ASN H 45 " pdb=" N GLU H 46 " pdb=" CA GLU H 46 " ideal model delta sigma weight residual 121.98 113.14 8.84 1.35e+00 5.49e-01 4.28e+01 angle pdb=" C ASN I 45 " pdb=" N GLU I 46 " pdb=" CA GLU I 46 " ideal model delta sigma weight residual 121.98 113.15 8.83 1.35e+00 5.49e-01 4.28e+01 angle pdb=" CA LEU F 150 " pdb=" CB LEU F 150 " pdb=" CG LEU F 150 " ideal model delta sigma weight residual 116.30 98.06 18.24 3.50e+00 8.16e-02 2.72e+01 ... (remaining 17471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 7462 16.96 - 33.92: 236 33.92 - 50.88: 27 50.88 - 67.84: 1 67.84 - 84.81: 5 Dihedral angle restraints: 7731 sinusoidal: 2988 harmonic: 4743 Sorted by residual: dihedral pdb=" CA SER E 117 " pdb=" C SER E 117 " pdb=" N GLU E 118 " pdb=" CA GLU E 118 " ideal model delta harmonic sigma weight residual -180.00 -150.43 -29.57 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA ASP A 230 " pdb=" C ASP A 230 " pdb=" N GLY A 231 " pdb=" CA GLY A 231 " ideal model delta harmonic sigma weight residual -180.00 -151.02 -28.98 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA ILE C 189 " pdb=" C ILE C 189 " pdb=" N PHE C 190 " pdb=" CA PHE C 190 " ideal model delta harmonic sigma weight residual -180.00 -151.22 -28.78 0 5.00e+00 4.00e-02 3.31e+01 ... (remaining 7728 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1167 0.037 - 0.074: 661 0.074 - 0.111: 263 0.111 - 0.148: 86 0.148 - 0.185: 12 Chirality restraints: 2189 Sorted by residual: chirality pdb=" CA VAL A 165 " pdb=" N VAL A 165 " pdb=" C VAL A 165 " pdb=" CB VAL A 165 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.59e-01 chirality pdb=" CB THR F 112 " pdb=" CA THR F 112 " pdb=" OG1 THR F 112 " pdb=" CG2 THR F 112 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.50e-01 chirality pdb=" CA VAL A 212 " pdb=" N VAL A 212 " pdb=" C VAL A 212 " pdb=" CB VAL A 212 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.18 2.00e-01 2.50e+01 8.46e-01 ... (remaining 2186 not shown) Planarity restraints: 2130 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 84 " 0.061 5.00e-02 4.00e+02 9.32e-02 1.39e+01 pdb=" N PRO B 85 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO B 85 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO B 85 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 212 " -0.049 5.00e-02 4.00e+02 7.44e-02 8.85e+00 pdb=" N PRO D 213 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO D 213 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 213 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 84 " 0.043 5.00e-02 4.00e+02 6.52e-02 6.79e+00 pdb=" N PRO C 85 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 85 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 85 " 0.036 5.00e-02 4.00e+02 ... (remaining 2127 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 260 2.60 - 3.17: 14293 3.17 - 3.75: 18354 3.75 - 4.32: 26776 4.32 - 4.90: 40002 Nonbonded interactions: 99685 Sorted by model distance: nonbonded pdb=" O ALA F 25 " pdb=" OG1 THR F 29 " model vdw 2.023 2.440 nonbonded pdb=" O THR A 62 " pdb=" OH TYR A 174 " model vdw 2.037 2.440 nonbonded pdb=" O LEU C 94 " pdb=" OG1 THR C 97 " model vdw 2.044 2.440 nonbonded pdb=" O THR C 62 " pdb=" OH TYR C 174 " model vdw 2.045 2.440 nonbonded pdb=" O THR C 49 " pdb=" OG1 THR C 52 " model vdw 2.074 2.440 ... (remaining 99680 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 99 5.16 5 C 8390 2.51 5 N 1934 2.21 5 O 2118 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.560 Check model and map are aligned: 0.200 Convert atoms to be neutral: 0.120 Process input model: 35.740 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.115 12820 Z= 0.641 Angle : 1.194 18.243 17476 Z= 0.599 Chirality : 0.054 0.185 2189 Planarity : 0.008 0.093 2130 Dihedral : 9.303 84.805 4637 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 26.32 Ramachandran Plot: Outliers : 0.68 % Allowed : 16.35 % Favored : 82.97 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.32 (0.14), residues: 1609 helix: -3.94 (0.09), residues: 1175 sheet: None (None), residues: 0 loop : -4.19 (0.25), residues: 434 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 448 time to evaluate : 1.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 454 average time/residue: 0.2603 time to fit residues: 163.4399 Evaluate side-chains 234 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 231 time to evaluate : 1.590 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1114 time to fit residues: 2.6703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 80 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 74 optimal weight: 0.5980 chunk 91 optimal weight: 20.0000 chunk 142 optimal weight: 0.5980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 GLN F 77 GLN F 165 ASN F 242 HIS F 262 ASN J 39 GLN ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 12820 Z= 0.250 Angle : 0.885 9.119 17476 Z= 0.440 Chirality : 0.047 0.253 2189 Planarity : 0.007 0.074 2130 Dihedral : 7.278 29.890 1695 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.83 % Favored : 90.74 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.19), residues: 1609 helix: -1.11 (0.14), residues: 1202 sheet: None (None), residues: 0 loop : -3.95 (0.26), residues: 407 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 361 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 362 average time/residue: 0.2351 time to fit residues: 122.0800 Evaluate side-chains 237 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 236 time to evaluate : 1.528 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1058 time to fit residues: 2.1886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 79 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 chunk 118 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 chunk 154 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 12820 Z= 0.227 Angle : 0.811 10.034 17476 Z= 0.399 Chirality : 0.045 0.249 2189 Planarity : 0.007 0.077 2130 Dihedral : 6.759 26.993 1695 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.68 % Allowed : 8.51 % Favored : 90.80 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.20), residues: 1609 helix: 0.09 (0.15), residues: 1208 sheet: None (None), residues: 0 loop : -3.86 (0.27), residues: 401 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 315 time to evaluate : 1.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 316 average time/residue: 0.2311 time to fit residues: 105.8043 Evaluate side-chains 225 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.529 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 141 optimal weight: 0.0970 chunk 107 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 151 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 chunk 40 optimal weight: 20.0000 chunk 126 optimal weight: 6.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 ASN ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.5187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 12820 Z= 0.239 Angle : 0.796 8.595 17476 Z= 0.391 Chirality : 0.045 0.164 2189 Planarity : 0.006 0.074 2130 Dihedral : 6.486 27.178 1695 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.68 % Allowed : 8.14 % Favored : 91.17 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.21), residues: 1609 helix: 0.44 (0.15), residues: 1196 sheet: None (None), residues: 0 loop : -3.59 (0.27), residues: 413 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 287 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 288 average time/residue: 0.2241 time to fit residues: 95.7668 Evaluate side-chains 224 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 1.852 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 86 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 104 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 136 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 ASN ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.5596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.073 12820 Z= 0.212 Angle : 0.760 8.463 17476 Z= 0.372 Chirality : 0.044 0.163 2189 Planarity : 0.006 0.065 2130 Dihedral : 6.231 25.856 1695 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.64 % Favored : 91.67 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.21), residues: 1609 helix: 0.71 (0.15), residues: 1201 sheet: None (None), residues: 0 loop : -3.42 (0.27), residues: 408 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 293 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 294 average time/residue: 0.2064 time to fit residues: 90.7491 Evaluate side-chains 223 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 1.412 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 136 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 37 optimal weight: 0.0570 chunk 151 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 79 optimal weight: 10.0000 chunk 146 optimal weight: 0.1980 overall best weight: 0.5902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.5953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 12820 Z= 0.196 Angle : 0.763 8.291 17476 Z= 0.369 Chirality : 0.043 0.161 2189 Planarity : 0.006 0.065 2130 Dihedral : 6.006 26.377 1695 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.68 % Allowed : 6.96 % Favored : 92.36 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.21), residues: 1609 helix: 0.93 (0.15), residues: 1191 sheet: None (None), residues: 0 loop : -3.12 (0.29), residues: 418 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.2181 time to fit residues: 97.5411 Evaluate side-chains 231 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 1.549 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 17 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 127 optimal weight: 9.9990 chunk 84 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 69 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.6258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 12820 Z= 0.193 Angle : 0.764 9.353 17476 Z= 0.367 Chirality : 0.043 0.171 2189 Planarity : 0.006 0.075 2130 Dihedral : 5.786 26.040 1695 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.21 % Favored : 92.11 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.21), residues: 1609 helix: 1.08 (0.15), residues: 1196 sheet: None (None), residues: 0 loop : -2.95 (0.30), residues: 413 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.2122 time to fit residues: 91.5541 Evaluate side-chains 216 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 1.411 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 60 optimal weight: 4.9990 chunk 90 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 14 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 137 optimal weight: 0.0980 chunk 144 optimal weight: 8.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN F 143 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.6370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 12820 Z= 0.215 Angle : 0.768 10.706 17476 Z= 0.370 Chirality : 0.044 0.170 2189 Planarity : 0.006 0.072 2130 Dihedral : 5.720 25.284 1695 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.40 % Favored : 91.98 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.21), residues: 1609 helix: 1.09 (0.15), residues: 1193 sheet: None (None), residues: 0 loop : -2.88 (0.30), residues: 416 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.2285 time to fit residues: 93.7366 Evaluate side-chains 217 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 1.579 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 0.7980 chunk 141 optimal weight: 4.9990 chunk 144 optimal weight: 0.9980 chunk 84 optimal weight: 0.2980 chunk 61 optimal weight: 8.9990 chunk 110 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 140 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN F 143 HIS F 182 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.6681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 12820 Z= 0.191 Angle : 0.773 9.230 17476 Z= 0.373 Chirality : 0.043 0.189 2189 Planarity : 0.006 0.075 2130 Dihedral : 5.619 25.973 1695 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.40 % Favored : 92.04 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.21), residues: 1609 helix: 1.15 (0.15), residues: 1190 sheet: None (None), residues: 0 loop : -2.88 (0.30), residues: 419 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 286 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 286 average time/residue: 0.2356 time to fit residues: 98.5740 Evaluate side-chains 214 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 1.567 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 149 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN C 76 ASN D 76 ASN E 76 ASN F 143 HIS ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.6632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 12820 Z= 0.257 Angle : 0.815 10.994 17476 Z= 0.394 Chirality : 0.046 0.299 2189 Planarity : 0.007 0.094 2130 Dihedral : 5.718 24.595 1695 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.58 % Favored : 91.80 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.22), residues: 1609 helix: 1.11 (0.15), residues: 1192 sheet: None (None), residues: 0 loop : -2.82 (0.31), residues: 417 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 262 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 262 average time/residue: 0.2017 time to fit residues: 79.1292 Evaluate side-chains 203 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 1.425 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.088234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.073346 restraints weight = 43887.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.075198 restraints weight = 27055.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.076321 restraints weight = 19185.608| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.6817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 12820 Z= 0.215 Angle : 0.800 10.137 17476 Z= 0.387 Chirality : 0.045 0.286 2189 Planarity : 0.006 0.076 2130 Dihedral : 5.614 24.789 1695 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.77 % Favored : 91.67 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.22), residues: 1609 helix: 1.14 (0.15), residues: 1196 sheet: None (None), residues: 0 loop : -2.87 (0.31), residues: 413 =============================================================================== Job complete usr+sys time: 2546.87 seconds wall clock time: 47 minutes 38.15 seconds (2858.15 seconds total)